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@@ -1,4 +1,4 @@ -<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:content="http://purl.org/rss/1.0/modules/content"><channel><title>Navan Chauhan</title><description>Welcome to my personal fragment of the internet. Majority of the posts should be complete.</description><link>https://navanchauhan.github.io/</link><language>en</language><lastBuildDate>Mon, 1 Jun 2020 12:27:03 +0530</lastBuildDate><pubDate>Mon, 1 Jun 2020 12:27:03 +0530</pubDate><ttl>250</ttl><atom:link href="https://navanchauhan.github.io/feed.rss" rel="self" type="application/rss+xml"/><item><guid isPermaLink="true">https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</guid><title>Workflow for Lightning Fast Molecular Docking Part One</title><description>This is my workflow for lightning fast molecular docking.</description><link>https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</link><pubDate>Mon, 1 Jun 2020 13:10:00 +0530</pubDate><content:encoded><![CDATA[<h1>Workflow for Lightning Fast Molecular Docking Part One</h1><h2>My Setup</h2><ul><li>macOS Catalina ( RIP 32bit app)</li><li>PyMOL</li><li>AutoDock Vina</li><li>Open Babel</li></ul><h2>One Command Docking</h2><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&&</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt +<?xml version="1.0" encoding="UTF-8"?><rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:content="http://purl.org/rss/1.0/modules/content"><channel><title>Navan Chauhan</title><description>Welcome to my personal fragment of the internet. Majority of the posts should be complete.</description><link>https://navanchauhan.github.io/</link><language>en</language><lastBuildDate>Mon, 1 Jun 2020 12:33:11 +0530</lastBuildDate><pubDate>Mon, 1 Jun 2020 12:33:11 +0530</pubDate><ttl>250</ttl><atom:link href="https://navanchauhan.github.io/feed.rss" rel="self" type="application/rss+xml"/><item><guid isPermaLink="true">https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</guid><title>Workflow for Lightning Fast Molecular Docking Part One</title><description>This is my workflow for lightning fast molecular docking.</description><link>https://navanchauhan.github.io/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL</link><pubDate>Mon, 1 Jun 2020 13:10:00 +0530</pubDate><content:encoded><![CDATA[<h1>Workflow for Lightning Fast Molecular Docking Part One</h1><h2>My Setup</h2><ul><li>macOS Catalina ( RIP 32bit app)</li><li>PyMOL</li><li>AutoDock Vina</li><li>Open Babel</li></ul><h2>One Command Docking</h2><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt <span class="o">&&</span> vina --receptor lu.pdbqt --center_x -9.7 --center_y <span class="m">11</span>.4 --center_z <span class="m">68</span>.9 --size_x <span class="m">19</span>.3 --size_y <span class="m">29</span>.9 --size_z <span class="m">21</span>.3 --ligand test.pdbqt </div></code></pre><p>To run this command you simple copy the SMILES structure of the ligand you want an it automatically takes it from your clipboard, generates the 3D structure in the AutoDock PDBQT format using Open Babel and then docks it with your receptor using AutoDock Vina, all with just one command.</p><p>Let me break down the commands</p><pre><code><div class="highlight"><span></span>obabel -:<span class="s2">"</span><span class="k">$(</span>pbpaste<span class="k">)</span><span class="s2">"</span> --gen3d -opdbqt -Otest.pdbqt </div></code></pre><p><code>pbpaste</code> and <code>pbcopy</code> are macOS commands for pasting and copying from and to the clipboard. Linux users may install the <code>xclip</code> and <code>xsel</code> packages from their respective package managers and then insert these aliases into their bash_profile, zshrc e.t.c</p><pre><code><div class="highlight"><span></span><span class="nb">alias</span> <span class="nv">pbcopy</span><span class="o">=</span><span class="s1">'xclip -selection clipboard'</span> <span class="nb">alias</span> <span class="nv">pbpaste</span><span class="o">=</span><span class="s1">'xclip -selection clipboard -o'</span> |